I have a tangerine and an orange tree both are very large in the front yard, last year my sister was doing some landscaping and decided to get rid of her lemon tree which was about 3 years old and producing very well. So, I figured I would plant it in my front yard. It didn't take long and the fruit was producing well, but it was orange in color. When cut into it smells like a tangerine, but still close to a lemon in taste. While at her house it was producing regular yellow lemons. I figure this is cross germination but is this common?
Your rootstock may have taken over your scions; this isn't uncommon. Most lemons that I grow are grafted onto Tangelo and Citrumelo roots (which are better) and occasionally when I have branches from below the graftline I have Tangelos and Lemons on the same plant.
I would say you are correct. Meyer lemons are best when used yellow or just turning yellow. They get a off flavor if left on the tree until they turn orange.